Speaking at the event organised by Scope, the cerebral palsy charity, in partnership with The TES, she said: "It is little short of cruelty to insist on ideological grounds that they should be subjected to the trauma of mainstream school."
The needs of children with autistic spectrum disorders could be met by a small caring primary school, but the transition to a large secondary school "could be disastrous", she said. They experienced problems with physical contact in busy corridors and dinner queues and also lacked the ability to respond to playground humour.
Children with emotional and behavioural difficulties also found it difficult in mainstream schools, she said, although the nurture group movement showed how small groups with teachers making constant contact "could make a huge difference."
Baroness Warnock, who led a major review of special education in the 1970s, also criticised the way in which good schools are encouraged to expand.
"Good schools will cease to be good schools if they double in size," she said.
Tara Flood, director of the Alliance for Inclusive Education, told the conference equality would only be achieved through inclusion for all children, whether or not they had an SEN label. She said that the voices of "special school survivors" were not heard loudly enough.
Another, panellist, Preethi Manuel, whose 18-year-old daughter with cerebral palsy had attended mainstream schools, said the whole school community benefited from inclusion.
A Scope survey of parents with disabled children showed 60 per cent said they had no choice of school for their child and 44 per cent were unhappy with that choice.
The conference preceded the second reading of the Education and Inspections Bill in the House of Lords. Richard Parnell, research and evidence manager of Scope, said that parental choice for disabled children will become an even greater struggle under the proposed legislation.
"Even this exploratory research makes it very clear that the parents of disabled children are getting a raw deal when it comes to choosing a school for their child."